scTC_eff_clr

Internal dataset containing marker gene effects using CLR transformation
(5 PCs, 1000 features) for evaluating trimming effects in scTrimClust.
Used by <code>scTC_trim_effect</code>.

internal

A toolkit for the analysis of high-dimensional repeated measurements, providing functions
for outlier detection, differential expression analysis, gene-set tests, and binary random data generation.

Klaus Jung

RepeatedHighDim

Methods for High-Dimensional Repeated Measures Data

Jochen Kruppa

Sergej Ruff

scTC_eff_clr function

A data frame with marker genes as rows and the following columns:<dl>
 <dt>CellAnnotation</dt>
<dd>Additional cell annotation information</dd> <dt>X</dt>
<dd>Row identifier</dd> <dt>avg_log2FC</dt>
<dd>Average log2 fold-change</dd> <dt>gene</dt>
<dd>Gene identifier</dd> <dt>p_val</dt>
<dd>Raw p-value</dd> <dt>p_val_adj</dt>
<dd>Adjusted p-value</dd> <dt>pct.1</dt>
<dd>Percentage of cells expressing the gene in cluster</dd> <dt>pct.2</dt>
<dd>Percentage of cells expressing the gene in other clusters</dd> <dt>cluster</dt>
<dd>Cluster assignment</dd>
</dl>

Format

COVID-19 CLR Transformation Marker Effects (Internal) — scTC_eff_clr

A data frame with marker genes as rows and the following columns:<dl>
 <dt>CellAnnotation</dt>
<dd>Additional cell annotation information</dd>

 <dt>X</dt>
<dd>Row identifier</dd>

 <dt>avg_log2FC</dt>
<dd>Average log2 fold-change</dd>

 <dt>gene</dt>
<dd>Gene identifier</dd>

 <dt>p_val</dt>
<dd>Raw p-value</dd>

 <dt>p_val_adj</dt>
<dd>Adjusted p-value</dd>

 <dt>pct.1</dt>
<dd>Percentage of cells expressing the gene in cluster</dd>

 <dt>pct.2</dt>
<dd>Percentage of cells expressing the gene in other clusters</dd>

 <dt>cluster</dt>
<dd>Cluster assignment</dd>


</dl>

scTC_eff_clr: COVID-19 CLR Transformation Marker Effects (Internal)

Description

Arguments

Format